A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
/home/runner/work/pmultiqc/pmultiqc/data
pmultiqc
pmultiqc is a MultiQC module to show the pipeline performance of mass spectrometry based quantification pipelines such as nf-core/quantms, MaxQuant, and DIA-NN.URL: https://github.com/bigbio/pmultiqc
Experimental Design and Metadata
Parameters
| No. | Parameter | Value |
|---|---|---|
| 1 | Version | 1.5.2.8 |
| 2 | User name | cbielow |
| 3 | Machine name | CD02-WIN7 |
| 4 | Date of writing | 08/05/2015 11:38:59 |
| 5 | Fixed modifications | Carbamidomethyl (C) |
| 6 | Decoy mode | revert |
| 7 | Special AAs | KR |
| 8 | Include contaminants | True |
| 9 | MS/MS tol. (FTMS) | 20 ppm |
| 10 | Top MS/MS peaks per 100 Da. (FTMS) | 12 |
| 11 | MS/MS deisotoping (FTMS) | True |
| 12 | MS/MS tol. (ITMS) | 0.5 Da |
| 13 | Top MS/MS peaks per 100 Da. (ITMS) | 8 |
| 14 | MS/MS deisotoping (ITMS) | False |
| 15 | MS/MS tol. (TOF) | 40 ppm |
| 16 | Top MS/MS peaks per 100 Da. (TOF) | 10 |
| 17 | MS/MS deisotoping (TOF) | True |
| 18 | MS/MS tol. (Unknown) | 0.5 Da |
| 19 | Top MS/MS peaks per 100 Da. (Unknown) | 8 |
| 20 | MS/MS deisotoping (Unknown) | False |
| 21 | PSM FDR | 0.0 |
| 22 | Protein FDR | 0.0 |
| 23 | Site FDR | 0.0 |
| 24 | Use Normalized Ratios For Occupancy | True |
| 25 | Min. peptide Length | 7 |
| 26 | Min. score for unmodified peptides | 0 |
| 27 | Min. score for modified peptides | 40 |
| 28 | Min. delta score for unmodified peptides | 0 |
| 29 | Min. delta score for modified peptides | 6 |
| 30 | Min. unique peptides | 0 |
| 31 | Min. razor peptides | 1 |
| 32 | Min. peptides | 1 |
| 33 | Use only unmodified peptides and | True |
| 34 | Modifications included in protein quantification | Acetyl (Protein N-term);Oxidation (M) |
| 35 | Peptides used for protein quantification | Razor |
| 36 | Discard unmodified counterpart peptides | True |
| 37 | Min. ratio count | 2 |
| 38 | Re-quantify | False |
| 39 | Use delta score | False |
| 40 | iBAQ | False |
| 41 | iBAQ log fit | False |
| 42 | Match between runs | True |
| 43 | Matching time window [min] | 0.7 |
| 44 | Alignment time window [min] | 20 |
| 45 | Find dependent peptides | False |
| 46 | Fasta file | crap_withMycoplasma.fasta;uniprot_human_canonical_and_isoforms_20130513.fasta |
| 47 | Labeled amino acid filtering | True |
| 48 | Site tables | Oxidation (M)Sites.txt |
| 49 | RT shift | False |
| 50 | Advanced ratios | True |
| 51 | First pass AIF correlation | 0.8 |
Results Overview
Summary Table
| #MS2 Spectra | #Identified MS2 Spectra | %Identified MS2 Spectra | #Peptides Identified | #Proteins Identified | #Proteins Quantified |
|---|---|---|---|---|---|
| 201567 | 84900 | 42.12% | 28949 | 4053 | 4048 |
HeatMap
Identification Summary
Number of Peptides identified Per Protein
ProteinGroups Count [MBR gain: +8.8%]
Peptide ID Count [MBR gain: +18.46%]
Missed Cleavages Per Raw File
Modifications Per Raw File
MS/MS Identified Per Raw File
Search Engine Scores
Summary of Andromeda Scores
Contaminants
Top5 Contaminants Per Raw File
Potential Contaminants Per File
Quantification Analysis
Peptides Quantification Table
| PeptideID | Protein Name | Peptide Sequence | Best Search Score | Average Intensity |
|---|---|---|---|---|
| 1 | Q86U42-2;Q86U42 | AAAAAAAAAAGAAGGR | 128.6800 | 7.1389 |
| 2 | P37108 | AAAAAAAAAPAAAATAPTTAATTAATAAQ | 82.8310 | 7.1284 |
| 3 | P36578 | AAAAAAALQAK | 135.4300 | 7.8269 |
| 4 | Q9H3H3-2;Q9H3H3-3 | AAAAAAAVAGVGR | 108.3100 | 6.4210 |
| 5 | Q96P70 | AAAAAAGAASGLPGPVAQGLK | 85.9370 | 6.6024 |
| 6 | P28482 | AAAAAAGAGPEMVR | 94.1220 | 6.4680 |
| 7 | Q8WVM8 | AAAAAATAAAAASIR | 146.5900 | 6.6441 |
| 8 | Q86X55-1;Q86X55;Q86X55-2 | AAAAAAVGPGAGGAGSAVPGGAGPCATVSVFPGAR | 59.5360 | 6.6710 |
| 9 | O00410 | AAAAAEQQQFYLLLGNLLSPDNVVR | 99.1100 | 6.7391 |
| 10 | O00410 | AAAAAEQQQFYLLLGNLLSPDNVVRK | 74.7030 | 6.7286 |
| 11 | P86791;P86790 | AAAAAGAGSGPWAAQEK | 82.9420 | 6.2996 |
| 12 | Q9Y2Z0-2;Q9Y2Z0 | AAAAAGTATSQR | 124.4200 | 7.5048 |
| 13 | Q7L5D6 | AAAAAMAEQESAR | 117.0300 | 6.0297 |
| 14 | Q13049 | AAAAASHLNLDALR | 88.7060 | 6.3835 |
| 15 | Q9P258 | AAAAAWEEPSSGNGTAR | 137.2700 | 6.1486 |
| 16 | O43324-2;O43324 | AAAAELSLLEK | 169.5200 | 6.9630 |
| 17 | Q96KQ7-2;Q96KQ7;Q96KQ7-3 | AAAAGAAAAAAAEGEAPAEMGALLLEK | 89.4620 | 5.9631 |
| 18 | Q00796 | AAAAKPNNLSLVVHGPGDLR | 112.8200 | 7.1325 |
| 19 | P55036 | AAAASAAEAGIATTGTEDSDDALLK | 54.0470 | 6.4029 |
| 20 | Q15005 | AAAAVQGGR | 127.4600 | 6.8615 |
| 21 | Q8N1G4 | AAAAVSESWPELELAER | 104.2100 | 6.1032 |
| 22 | O00231;O00231-2 | AAAAVVEFQR | 105.9800 | 6.9886 |
| 23 | Q8NI27 | AAAAVVVPAEWIK | 59.2270 | 6.5836 |
| 24 | P30153 | AAADGDDSLYPIAVLIDELR | 85.2030 | 6.1322 |
| 25 | Q9UNF1-2;Q9UNF1 | AAAEAAAEAK | 91.7010 | 5.2648 |
| 26 | Q9NQP4 | AAAEDVNVTFEDQQK | 147.7500 | 5.9965 |
| 27 | P55263;P55263-3 | AAAEEEPKPK | 86.8980 | 6.2054 |
| 28 | Q99567 | AAAEGPVGDGELWQTWLPNHVVFLR | 80.2360 | 6.2906 |
| 29 | Q13523 | AAAETQSLR | 76.1700 | 6.4857 |
| 30 | P02786 | AAAEVAGQFVIK | 117.2000 | 6.6548 |
| 31 | Q9Y490 | AAAFEEQENETVVVK | 130.4700 | 6.2308 |
| 32 | O94826 | AAAFEQLQK | 78.5560 | 6.9091 |
| 33 | P35221;P35221-2 | AAAGEFADDPCSSVK | 120.2100 | 6.7622 |
| 34 | Q96C19 | AAAGELQEDSGLCVLAR | 170.4700 | 6.5967 |
| 35 | Q9UL25 | AAAGGGGGGAAAAGR | 182.7100 | 6.7549 |
| 36 | Q96T51;Q96T51-3 | AAAGLGGGDSGDGTAR | 108.6600 | 6.6020 |
| 37 | P51970 | AAAHHYGAQCDKPNK | 44.4360 | 5.2035 |
| 38 | P08107;P08107-2 | AAAIGIDLGTTYSCVGVFQHGK | 60.0620 | 6.7559 |
| 39 | Q14008-2;Q14008;Q14008-3 | AAALATVNAWAEQTGMK | 172.4200 | 6.1280 |
| 40 | P31948 | AAALEFLNR | 82.2870 | 6.3951 |
| 41 | P31948 | AAALEFLNRFEEAK | 137.8100 | 7.3349 |
| 42 | O60716-13;O60716-11;O60716-10;O60716-9;O60716-21;O60716-19;O60716-16;O60716-18;O60716-15;O60716-17;O60716-14;O60716-12;O60716-5;O60716-3;O60716-2;O60716;O60716-24;O60716-23;O60716-22;O60716-20;O60716-8;O60716-7;O60716-6;O60716-4;O60716-29;O60716-27;O60716-26;O60716-25;O60716-32;O60716-31;O60716-30;O60716-28 | AAALVLQTIWGYK | 145.8100 | 6.3166 |
| 43 | Q14498-2;Q14498;Q14498-3 | AAAMANNLQK | 73.2330 | 5.4044 |
| 44 | P62877 | AAAMDVDTPSGTNSGAGK | 168.4200 | 5.9619 |
| 45 | P62877 | AAAMDVDTPSGTNSGAGKK | 186.7200 | 6.6983 |
| 46 | Q9NX63 | AAANEQLTR | 107.4500 | 6.4553 |
| 47 | P26641 | AAAPAPEEEMDECEQALAAEPK | 131.5600 | 6.6380 |
| 48 | P20810-7;P20810-6;P20810-5;P20810-4;P20810-8;P20810;P20810-2;P20810-3 | AAAPAPVSEAVCR | 90.7930 | 7.3560 |
| 49 | Q12765 | AAAPPSYCFVAFPPR | 56.5690 | 5.7088 |
| 50 | P53618 | AAAQCYIDLIIK | 77.6440 | 6.8017 |
Protein Quantification Table
| ProteinID | Protein Name | Number of Peptides | Average Intensity |
|---|---|---|---|
| 1 | A0AV96-2;A0AV96 | 2 | 5.8834 |
| 2 | A0AVT1 | 1 | 6.9224 |
| 3 | A0AVT1;A0AVT1-2 | 19 | 6.4333 |
| 4 | A0AVT1;A0AVT1-3 | 1 | 6.0380 |
| 5 | A0AVT1;A0AVT1-3;A0AVT1-4 | 6 | 6.3704 |
| 6 | A0FGR8-2 | 1 | 5.4654 |
| 7 | A0FGR8-2;A0FGR8;A0FGR8-6 | 1 | 5.5375 |
| 8 | A0FGR8-2;A0FGR8;A0FGR8-6;A0FGR8-4 | 6 | 6.5283 |
| 9 | A0FGR8-2;A0FGR8;A0FGR8-6;A0FGR8-4;A0FGR8-5 | 1 | 6.6685 |
| 10 | A0FGR8-2;A0FGR8;A0FGR8-6;A0FGR8-5 | 4 | 6.4869 |
| 11 | A0MZ66-2;A0MZ66-8;A0MZ66-4;A0MZ66-5;A0MZ66-6;A0MZ66;A0MZ66-3 | 2 | 6.2240 |
| 12 | A1L0T0 | 12 | 6.3070 |
| 13 | A2RRP1-2;A2RRP1 | 3 | 5.7738 |
| 14 | A4D1E9 | 1 | 5.7467 |
| 15 | A4D1E9;A4D1E9-2 | 1 | 6.2192 |
| 16 | A4UGR9-2;A4UGR9-3;A4UGR9 | 1 | 6.4718 |
| 17 | A5D8W1-2;A5D8W1-5;A5D8W1 | 1 | 6.5837 |
| 18 | A5D8W1-2;A5D8W1-5;A5D8W1;A5D8W1-4;A5D8W1-3 | 1 | 6.5649 |
| 19 | A5YKK6-2;A5YKK6 | 1 | 6.1066 |
| 20 | A5YKK6-2;A5YKK6;A5YKK6-3 | 4 | 5.8559 |
| 21 | A5YKK6-2;A5YKK6;A5YKK6-3;A5YKK6-4 | 4 | 6.0792 |
| 22 | A6NDG6 | 4 | 6.1718 |
| 23 | A6NDU8 | 1 | 6.1976 |
| 24 | A6NFZ4 | 1 | 5.3669 |
| 25 | A6NHL2-2;A6NHL2 | 1 | 6.6717 |
| 26 | A6NHQ2 | 1 | 6.9258 |
| 27 | A6NHR9 | 1 | 6.3482 |
| 28 | A6NHR9;A6NHR9-2 | 9 | 6.1953 |
| 29 | A6NHR9;A6NHR9-2;A6NHR9-3 | 6 | 6.3258 |
| 30 | A6NKF9;B7ZAQ6-2;B7ZAQ6-3;P0CG08;B7ZAQ6 | 1 | 5.9271 |
| 31 | A6NKT7;Q7Z3J3 | 1 | 5.9068 |
| 32 | A6NKT7;Q7Z3J3;P0DJD0;P0DJD1;Q8IWJ2 | 1 | 5.6636 |
| 33 | A8MT69 | 1 | 5.4836 |
| 34 | A8MXV4 | 3 | 6.2205 |
| 35 | C9JLW8 | 1 | 6.1450 |
| 36 | CONTAMINANT_sp|ANXA5_HUMAN|;P08758 | 25 | 7.4325 |
| 37 | CONTAMINANT_sp|B2MG_HUMAN|;P61769 | 3 | 7.6794 |
| 38 | CONTAMINANT_sp|BID_HUMAN|;P55957;P55957-2 | 1 | 5.7736 |
| 39 | CONTAMINANT_sp|BID_HUMAN|;P55957;P55957-2;P55957-3 | 1 | 6.5969 |
| 40 | CONTAMINANT_sp|BID_HUMAN|;P55957;P55957-2;P55957-4 | 4 | 6.2732 |
| 41 | CONTAMINANT_sp|CATA_HUMAN|;P04040 | 13 | 6.7989 |
| 42 | CONTAMINANT_sp|CATD_HUMAN|;P07339 | 21 | 7.2581 |
| 43 | CONTAMINANT_sp|CYC_HUMAN|;P99999 | 5 | 6.9857 |
| 44 | CONTAMINANT_sp|CYC_HUMAN|;P99999;CONTAMINANT_sp|CYC_HORSE|;CON__P62894 | 2 | 7.0820 |
| 45 | CONTAMINANT_sp|NEDD8_HUMAN|;Q15843 | 2 | 6.6189 |
| 46 | CONTAMINANT_sp|NQO2_HUMAN|;P16083 | 2 | 6.4140 |
| 47 | CONTAMINANT_sp|PRDX1_HUMAN|;Q06830 | 12 | 7.8054 |
| 48 | CONTAMINANT_sp|PRDX1_HUMAN|;Q06830;P32119 | 1 | 8.0652 |
| 49 | CONTAMINANT_sp|PRDX1_HUMAN|;Q06830;Q13162 | 2 | 7.8547 |
| 50 | CONTAMINANT_sp|RS27A_HUMAN|;P62979 | 2 | 7.2087 |